The out-of-universe explanation is that the original design of the character was based on circus strongmen (thus the tights and underwear on the outside combo), and he wasn't portrayed as strong as he eventually became. "Being able to pick up a small car" doesn't mean he could easily pick up anything else, so exercising to be even stronger makes sense. Of course, this made no sense by the Silver Age when he had obscene amounts of power and had such since he was a baby, but at that point the design of him had pretty much been set.
The other explanation is that most artists had one standard "heroic build" that they used for pretty much any character, so it didn't matter what their powerset was. There's no reason Hal Jordan should be built like a strongman either; test pilots may be fit but they generally don't look like bodybuilders.
In universe, the idea that's been around since the 1980s is that Superman didn't have all his power right from the start; it took time to develop as he grew up, and part of that maturation process was to become extremely fit as he physically developed, and he could have been pushing his limits as his powers grew, so by the time his powers reached the point where pushing himself to improve became silly, his body had already developed.
The last possibility isn't one I can recall seeing, but it's probably been used: Kal-El comes from a planet with high technology, including biological sciences. It's possible being so developed is simply in his genes and Kryptonians engineered themselves to look that way.